Summary: The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs

This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.

The Science Page this week describes a study done by Tara N. Gaire, Carissa Odland, Bingzhou Zhang, Tui Ray, Enrique Doster, Joel Nerem, Scott Dee, Peter Davies and Noelle Noyes and sheds some light on the antimicrobial resistances carried by the pig’s microbiome after disease and treatment.

Continue readingSummary: The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs

The Resistome: What is it, and why should I care? Part 2

Last week, we talked about the resistome – what it is, and what it could mean for livestock production and public policy. If you need a quick reminder, check back to last week’s MSHMP report before continuing.

This week, we continue our list of five emerging trends about the resistome:

3. Growing animals experience dramatic changes in their resistome, even in the absence of antibiotic drugs. This is also true for human babies and children.In fact, the scientific literature is clear on this: the resistome (and also the microbiome!) of rapidly growing livestock animals is dynamic. For the swine world, this means that most of our antibiotic treatments are being given to animals whose resistance (and microbiome) profiles are already in a baseline state of flux. Contrast this to human medicine, where we have the luxury of studying resistance in very mature, stable populations; not so in swine medicine. While that means that our task might be more challenging, I am optimistic that it also presents exciting opportunities. Given that the microbiome (and resistome) of growing animals is already changing dramatically, do we have an opportunity to “nudge” it in one direction or the other? There is some evidence that the microbiomes of adult humans are surprisingly resilient, i.e., they may shift transiently but often return to their “normal” state. This resilience might be a good thing for most of us, but it makes it challenging to change our microbiomes permanently if we need to. Perhaps because growing animals’ microbiomes are not so stable, we can more easily nudge them towards a beneficial state, i.e., with more metabolically- and inflammatory-friendly microbes and fewer resistance genes? We don’t know yet, but it’s an intriguing question.

4. Resistance is even more complex than we realize, and this is a good thing. Given everything I’ve outlined above, it should be no surprise that some of our assumptions about antibiotic resistance are being challenged. This is a good thing, and I’m hopeful that eventually this newfound knowledge will allow us to protect antibiotic efficacy in the long-term. Bacteria will always find a way to resist our treatments, and therefore the antibiotic pipeline must run continually to keep up.If there are ways that we can manipulate bacterial populations to slow down their evolution towards resistance, this prolongs the efficacy of antibiotics that are already on the market. I think that the complex resistome dynamics that we can now leverage are likely to hold some solutions in this regard.

5. Resistome (and microbiome) data is exploding – faster than we can keep up. Given the relative ease with which we can now generate DNA sequence data, we are experience a “data deluge”. While data generation is a necessary step towards knowledge discovery, it is not a sufficient step. We need to make sure that we are taking the laborious and resource-intensive measures needed to turn this data into information, and then finally into applied benefit. This transformation requires a dedicated team of extremely diverse skillsets – and that team includes producers and veterinarians who can help us ask the right questions of the data, and can then help us turn the resulting information into on-farm benefit.

I’m sure this science report is a bit different than what you expected to read, but I hope it was a helpful essay on the resistome and all of its complexities.

If you want to read some of our livestock-related scientific literature that utilizes a resistome approach, I would encourage you to read the following research summaries:

Summary 1

Summary 2

There are also some podcasts and blogs about our work, which can be found here: podcast and blog post.

And finally, you can always see our latest research publications and activities at our website and Twitter accounts: and @noelle_noyes

Thanks for reading!

The Resistome: What is it, and why should I care?

This week, we are sharing the first part of a report on the resistome by Dr. Noelle Noyes.

Did you know that you currently have dozens – maybe even hundreds – of antimicrobial resistance genes in, on and around your body? While this sounds alarming, it is probably normal. In fact, scientists have identified antimicrobial resistance genes in places as remote as the Antarctic permafrost, and even in the frozen stomach contents of “Ötzi” the Iceman (who certainly didn’t benefit from modern antibiotics)! We term this universal collection of antimicrobial resistance genes the “resistome”. It is just like the “microbiome” (aka the collection of microbes in our world)- – but for antimicrobial resistance.

To understand research that uses the resistome, I first need to give a short primer – so bear with me! Antimicrobial resistance is generally thought of as the ability of microbes to resist the effects of antibiotic drugs. In the past, researchers have studied antibiotic resistance by growing (or “culturing”) a pathogen in a Petri dish, and then bathing the pathogens in an antibiotic drug. If the pathogens are able to grow in the antibiotic, they are termed “resistant”. This approach yields useful information, especially if a doctor or veterinarian is trying to treat a patient that has an illness caused by a specific pathogen. However, our bodies, homes and environments contain thousands of different microbes – the pathogen making us sick is just one of these thousands. Therefore, when we limit our investigation to a single pathogen, we are missing thousands of bacteria that may also be carrying resistance DNA.

Today, we can overcome this limitation by harvesting all of the microbial DNA in a sample and “reading” it using a next-generation sequencing machine.Just like you can have your own human DNA sequenced, we can also sequence the DNA of all of the microbes that inhabit your body, home, pets or farm.Once we sequence this DNA, we can then look at it closely to identify all of the resistance genes that are present – this is the “resistome” of the sample.Of course, it takes supercomputers and bioinformatics to accomplish this task, but many scientists are now performing these types of analyses on a fairly routine basis.

The big question is: who cares? What does all of this DNA and the resistome mean for animal production? Or even human health? Well, this is early days for resistome research, and therefore those questions are still being answered (and probably will be for the foreseeable future). However, in our own research, we have found some emerging trends that I believe have some important implications for the work that you do on your farm, as well as policy development, and public, human and animal health. In this MSHMP report, I will detail two of these five trends, and stay tuned for the next three!

1. The resistome is everywhere, and it usually contains many dozens (and sometimes hundreds and thousands) of unique resistance genes. As I mentioned earlier, resistance genes have been identified in numerous and diverse “pristine” environments, such as caves that have been untouched by humans for thousands of years, or the feces of remote, indigenous human populations where antibiotics have not been used; resistance DNA is found commonly in the meconium of newborn infants and animals. Given all of this evidence, there is now a strong consensus that the DNA that codes for antibiotic resistance is a “natural phenomenon”, and that this “natural” resistome can be very diverse. So why does this matter? Well, it makes it tricky to define a baseline, and therefore tricky to identify specific management practices that might be causing the resistome to become “worse”. Every veterinarian knows: if you can’t define normal, it’s hard to define abnormal.

2. The resistome that we detect in a sample is determined largely by the microbiome in that same sample. This might seem intuitive, but it has important implications for resistance research and control. Because what this means is that anything that we do to change the microbiome will most likely have a big impact on the resistome as well. And many things can change the microbiome, including changing our diet, moving to a new home (or farm), undergoing stress, getting sick, and becoming pregnant. Therefore, if any of these changes are occurring in our herd, we should expect to see changes in the resistome profiles of our animals. And as producers and veterinarians, I’m sure you realize that most of your livestock are undergoing at least one (if not multiple) of these “life events” nearly every day. So if we want to understand specifically how antibiotic use impacts resistance in our herd, we need to take into account all of these other things that might be occurring in our livestock at the time of antibiotic administration. By the same token, we need to realize that experimental conditions (for instance, putting animals in small groups in a research facility) may induce microbiome (and thus resistome) shifts that are completely different than those we would see in commercial production. Certainly such experimental studies are a rational and solid starting point, and I don’t want to discredit their utility; however, in order to develop meaningful and concrete policies and guidelines, I believe we need well-controlled, large-scale studies in livestock animals being raised under true commercial conditions.Without such studies, it is impossible to generate practical, evidence-based guidelines regarding antibiotic use and resistance. And in the absence of evidence, it is all too easy for people to react out of fear, which can result in irrational and/or ineffective policy. This point is especially significant as scrutiny over preventive antibiotic uses grows.

Check back next week for points 3, 4 and 5!

And in the meantime, the following links contain research summaries from studies that have utilized a resistome approach in commercial livestock populations:

Summary 1

Summary 2